9ZCC | pdb_00009zcc

1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle type-2 dimer

• PDB DOI: https://doi.org/10.2210/pdb9ZCC/pdb
• EM Map EMD-70040: EMDB EMDataResource
• NAKB: 9ZCC

• Classification: RNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2025-11-22 Released: 2025-12-03 
• Deposition Author(s): McRae, E.K.S., Yadav, D.K.
• Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 12.2 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Base modifications reshape RNA folding landscapes and structure function relationships in synthetic and natural RNAs

Kumar, D.Y., Yang, H., Lee, S., McRae, E.K.S.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 475.48 kDa 
• Atom Count: 31,464 
• Modeled Residue Count: 1,460 
• Deposited Residue Count: 1,460 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle	A [auth B], B [auth A]	730	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 12.2 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): McRae, E.K.S., Yadav, D.K.

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Funding Organization	Location	Grant Number
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR230015

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release